updated tests for DB selection

locidex/extract.py

@@ -15,7 +15,7 @@
 from locidex.constants import SEARCH_RUN_DATA, FILE_TYPES, BLAST_TABLE_COLS, DBConfig, DB_EXPECTED_FILES, NT_SUB, EXTRACT_MODES, OPTION_GROUPS
 from locidex.version import __version__
 from locidex.classes.aligner import perform_alignment, aligner
-import locidex.manifest as manifest
+from locidex.utils import check_db_groups
 
 def add_args(parser=None):
     if parser is None:
@@ -263,16 +263,7 @@ def run(cmd_args=None):
 
     analysis_parameters = vars(cmd_args)
 
-    for opt in OPTION_GROUPS:
-        if analysis_parameters[opt] is not None:
-            for option in OPTION_GROUPS[opt]:
-                if analysis_parameters[option] is None:
-                    raise AttributeError("Missing required parameter: {}".format(option))
-
-    if cmd_args.db_group is not None:
-        analysis_parameters["db"] = str(manifest.get_manifest_db(input_file=Path(cmd_args.db_group), name=cmd_args.db_name, version=cmd_args.db_version))
-
-
+    analysis_parameters = check_db_groups(analysis_params=analysis_parameters, cmd_args=cmd_args)
 
     config_file = cmd_args.config
 

locidex/search.py

@@ -8,12 +8,11 @@
 
 import pandas as pd
 
-import locidex.manifest as manifest
 from locidex.classes.blast import blast_search, parse_blast
 from locidex.classes.db import search_db_conf, db_config
 from locidex.classes.seq_intake import seq_intake, seq_store
 from locidex.constants import SEARCH_RUN_DATA, FILE_TYPES, BLAST_TABLE_COLS, DB_EXPECTED_FILES, OPTION_GROUPS, DBConfig
-from locidex.utils import write_seq_dict
+from locidex.utils import write_seq_dict, check_db_groups
 from locidex.version import __version__
 
 def add_args(parser=None):
@@ -302,16 +301,9 @@ def run(cmd_args=None):
         parser = add_args()
         cmd_args = parser.parse_args()
     analysis_parameters = vars(cmd_args)
-
-    for opt in OPTION_GROUPS:
-        if analysis_parameters[opt] is not None:
-            for option in OPTION_GROUPS[opt]:
-                if analysis_parameters[option] is None:
-                    raise AttributeError("Missing required parameter: {}".format(option))
-
-    if cmd_args.db_group is not None:
-        analysis_parameters["db"] = str(manifest.get_manifest_db(input_file=Path(cmd_args.db_group), name=cmd_args.db_name, version=cmd_args.db_version))
 
+    analysis_parameters = check_db_groups(analysis_params=analysis_parameters, cmd_args=cmd_args)
+
     config_file = cmd_args.config
 
     config = {}

locidex/utils.py

@@ -1,12 +1,29 @@
 import hashlib
 import json
 import os
+import argparse
 from collections import Counter
+from pathlib import Path
 
 from Bio.Seq import Seq
 
-from locidex.constants import NT_SUB, PROTEIN_ALPHA, DNA_ALPHA
+from locidex.constants import NT_SUB, PROTEIN_ALPHA, DNA_ALPHA, OPTION_GROUPS
+import locidex.manifest as manifest 
 
+def check_db_groups(analysis_params: dict, cmd_args: argparse.Namespace, param_db: str = "db") -> dict:
+    """
+    Verify that a locidex database, or database group passed has all of the require parameters
+    """
+    for opt in OPTION_GROUPS:
+        if analysis_params[opt] is not None:
+            for option in OPTION_GROUPS[opt]:
+                if analysis_params[option] is None:
+                    raise AttributeError("Missing required parameter: {}".format(option))
+
+    if cmd_args.db_group is not None:
+        analysis_params[param_db] = str(manifest.get_manifest_db(input_file=Path(cmd_args.db_group), name=cmd_args.db_name, version=cmd_args.db_version))
+
+    return analysis_params
 
 def revcomp(s):
     """

tests/test_utils.py

@@ -0,0 +1,26 @@
+"""
+Test the ever growing util functions
+"""
+
+import pytest
+from locidex import utils
+from locidex import manifest
+from argparse import Namespace
+
+
+def test_check_db_groups_pass(monkeypatch):
+    nm_group = Namespace(db_group="Db1", db_name="test_name", db_version="1.0.0")
+    analysis_params = {"db_group": "Db1", "db_name": "test_name", "db_version": "1.0.0"}
+
+    def mockreturn(*args, **kwargs):
+        return True
+    monkeypatch.setattr(manifest, "get_manifest_db", mockreturn)
+    analysis_params = utils.check_db_groups(analysis_params, nm_group)
+    assert analysis_params["db"]
+
+def test_check_db_groups_fail():
+    nm_group = Namespace(db_group="Db1", db_name="test_name", db_version="1.0.0")
+    analysis_params = {"db_group": "Db1", "db_name": "test_name"}
+
+    with pytest.raises(KeyError):
+        analysis_params = utils.check_db_groups(analysis_params, nm_group)